libSBML Python API
5.10.0
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{fbc}
fbc Implementation of the 'fbc' package extention to the Model construct.Public Member Functions | |
def | addFluxBound |
def | addGeneAssociation |
def | addObjective |
def | clone |
def | createFluxBound |
def | createGeneAssociation |
def | createObjective |
def | getActiveObjective |
def | getActiveObjectiveId |
def | getElementByMetaId |
def | getElementBySId |
def | getElementNamespace |
def | getFluxBound |
def | getFluxBoundsForReaction |
def | getGeneAssociation |
def | getLevel |
def | getListOfAllElements |
def | getListOfFluxBounds |
def | getListOfGeneAssociations |
def | getListOfObjectives |
def | getNumFluxBounds |
def | getNumGeneAssociations |
def | getNumObjectives |
def | getObjective |
def | getPackageName |
def | getPackageVersion |
def | getParentSBMLObject |
def | getPrefix |
def | getSBMLDocument |
def | getURI |
def | getVersion |
def | removeFluxBound |
def | removeGeneAssociation |
def | removeObjective |
def | setActiveObjectiveId |
def | setElementNamespace |
def | unsetActiveObjectiveId |
def libsbml.FbcModelPlugin.addFluxBound | ( | self, | |
args | |||
) |
Python method signature(s):
addFluxBound(FbcModelPlugin self, FluxBound bound)int
Adds a copy of the given FluxBound object to the list of FluxBounds.
bound | the FluxBound object to be added to the list of FluxBounds. |
def libsbml.FbcModelPlugin.addGeneAssociation | ( | self, | |
args | |||
) |
Python method signature(s):
addGeneAssociation(FbcModelPlugin self, GeneAssociation association)int
Adds a copy of the given GeneAssociation object to the list of GeneAssociations.
association | the GeneAssociation object to be added to the list of GeneAssociations. |
def libsbml.FbcModelPlugin.addObjective | ( | self, | |
args | |||
) |
Python method signature(s):
addObjective(FbcModelPlugin self, Objective bound)int
Adds a copy of the given Objective object to the list of Objectives.
bound | the Objective object to be added to the list of Objectives. |
def libsbml.FbcModelPlugin.clone | ( | self | ) |
{fbc}
fbc Implementation of the 'fbc' package extention to the Model construct. Python method signature(s):clone(FbcModelPlugin self)FbcModelPlugin
Creates and returns a deep copy of this FbcModelPlugin object.
def libsbml.FbcModelPlugin.createFluxBound | ( | self | ) |
Python method signature(s):
createFluxBound(FbcModelPlugin self)FluxBound
Creates a new FluxBound object and adds it to the list of FluxBound objects and returns it.
def libsbml.FbcModelPlugin.createGeneAssociation | ( | self | ) |
Python method signature(s):
createGeneAssociation(FbcModelPlugin self)GeneAssociation
Creates a new GeneAssociation object and adds it to the list of GeneAssociation objects and returns it.
def libsbml.FbcModelPlugin.createObjective | ( | self | ) |
Python method signature(s):
createObjective(FbcModelPlugin self)Objective
Creates a new Objective object and adds it to the list of Objective objects and returns it.
def libsbml.FbcModelPlugin.getActiveObjective | ( | self, | |
args | |||
) |
Python method signature(s):
getActiveObjective(FbcModelPlugin self)Objective getActiveObjective(FbcModelPlugin self)
Objective
Returns the current active objective.
def libsbml.FbcModelPlugin.getActiveObjectiveId | ( | self | ) |
Python method signature(s):
getActiveObjectiveId(FbcModelPlugin self)string
returns the id of the current active objective.
def libsbml.FbcModelPlugin.getElementByMetaId | ( | self, | |
args | |||
) |
Python method signature(s):
getElementByMetaId(FbcModelPlugin self, string metaid)SBase
Returns the first child element it can find with the given metaid
, or itself if it has the given metaid
, or None
if no such object is found.
metaid | string representing the metaid of objects to find |
metaid
. def libsbml.FbcModelPlugin.getElementBySId | ( | self, | |
args | |||
) |
Python method signature(s):
getElementBySId(FbcModelPlugin self, string id)SBase
Returns the first child element found that has the given id
in the model-wide SId namespace, or None
if no such object is found.
id | string representing the id of objects to find |
id
.
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inherited |
{core}
Representation of a plug-in object of SBML's package extension.Additional attributes and/or elements of a package extension which are directly contained by some pre-defined element are contained/accessed by SBasePlugin class which is extended by package developers for each extension point. The extension point, which represents an element to be extended, is identified by a combination of a Package name and a typecode of the element, and is represented by SBaseExtensionPoint class.
For example, the layout extension defines <listOfLayouts> element which is directly contained in <model> element of the core package. In the layout package (provided as one of example packages in libSBML-5), the additional element for the model element is implemented as ListOfLayouts class (an SBase derived class) and the object is contained/accessed by a LayoutModelPlugin class (an SBasePlugin derived class).
SBasePlugin class defines basic virtual functions for reading/writing/checking additional attributes and/or top-level elements which should or must be overridden by subclasses like SBase class and its derived classes.
Package developers must implement an SBasePlugin exntended class for each element to be extended (e.g. SBMLDocument, Model, ...) in which additional attributes and/or top-level elements of the package extension are directly contained.
To implement reading/writing functions for attributes and/or top-level elements of the SBsaePlugin extended class, package developers should or must override the corresponding virtual functions below provided in the SBasePlugin class:
reading elements :
virtual SBase createObject (XMLInputStream stream)
This function must be overridden if one or more additional elements are defined.
virtual bool readOtherXML (SBase parentObject, XMLInputStream stream)
This function should be overridden if elements of annotation, notes, MathML, etc. need to be directly parsed from the given XMLInputStream object.
reading attributes (must be overridden if additional attributes are defined) :
virtual void addExpectedAttributes(ExpectedAttributes& attributes)
virtual void readAttributes (XMLAttributes attributes, ExpectedAttributes& expectedAttributes)
writing elements (must be overridden if additional elements are defined) :
virtual void writeElements (XMLOutputStream stream)
writing attributes :
virtual void writeAttributes (XMLOutputStream stream)
This function must be overridden if one or more additional attributes are defined.
virtual void writeXMLNS (XMLOutputStream stream)
This function must be overridden if one or more additional xmlns attributes are defined.
checking elements (should be overridden) :
virtual bool hasRequiredElements()
checking attributes (should be overridden) :
virtual bool hasRequiredAttributes()
To implement package-specific creating/getting/manipulating functions of the SBasePlugin derived class (e.g., getListOfLayouts(), createLyout(), getLayout(), and etc are implemented in LayoutModelPlugin class of the layout package), package developers must newly implement such functions (as they like) in the derived class.
SBasePlugin class defines other virtual functions of internal implementations such as:
virtual void setSBMLDocument(SBMLDocument d)
virtual void connectToParent(SBasesbase)
virtual void enablePackageInternal(string pkgURI, string pkgPrefix, bool flag)
These functions must be overridden by subclasses in which one or more top-level elements are defined.
For example, the following three SBasePlugin extended classes are implemented in the layout extension:
SBMLDocumentPlugin class for SBMLDocument element
(SBMLDocumentPlugin class is a common SBasePlugin extended class for SBMLDocument class. Package developers can use this class as-is if no additional elements/attributes (except for required attribute) is needed for the SBMLDocument class in their packages, otherwise package developers must implement a new SBMLDocumentPlugin derived class.)
LayoutModelPlugin class for Model element
<listOfLayouts> element is added to Model object.
The following virtual functions for reading/writing/checking are overridden: (type of arguments and return values are omitted)
createObject()
: (read elements) readOtherXML()
: (read elements in annotation of SBML L2) writeElements()
: (write elements) The following virtual functions of internal implementations are overridden: (type of arguments and return values are omitted)
setSBMLDocument()
connectToParent()
enablePackageInternal()
The following creating/getting/manipulating functions are newly implemented: (type of arguments and return values are omitted)
getListOfLayouts()
getLayout ()
addLayout()
createLayout()
removeLayout()
getNumLayouts()
LayoutSpeciesReferencePlugin class for SpeciesReference element (used only for SBML L2V1)
id attribute is internally added to SpeciesReference object only for SBML L2V1
The following virtual functions for reading/writing/checking are overridden: (type of arguments and return values are omitted)
readOtherXML()
writeAttributes()
Python method signature(s):
getElementNamespace(SBasePlugin self)string
Returns the XML namespace (URI) of the package extension of this plugin object.
def libsbml.FbcModelPlugin.getFluxBound | ( | self, | |
args | |||
) |
Python method signature(s):
getFluxBound(FbcModelPlugin self, long n)FluxBound getFluxBound(FbcModelPlugin self, long n)
FluxBound getFluxBound(FbcModelPlugin self, string sid)
FluxBound getFluxBound(FbcModelPlugin self, string sid)
FluxBound
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
getFluxBound(long n)
Returns the FluxBound object that belongs to the given index. If the index is invalid, None
is returned.
n | the index number of the FluxBound to get. |
getFluxBound(string sid)
Returns the FluxBound object based on its identifier.
sid | a string representing the identifier of the FluxBound to get. |
sid
or None if no such FluxBound exists.def libsbml.FbcModelPlugin.getFluxBoundsForReaction | ( | self, | |
args | |||
) |
Python method signature(s):
getFluxBoundsForReaction(FbcModelPlugin self, string reaction)ListOfFluxBounds
def libsbml.FbcModelPlugin.getGeneAssociation | ( | self, | |
args | |||
) |
Python method signature(s):
getGeneAssociation(FbcModelPlugin self, long n)GeneAssociation getGeneAssociation(FbcModelPlugin self, long n)
GeneAssociation getGeneAssociation(FbcModelPlugin self, string sid)
GeneAssociation getGeneAssociation(FbcModelPlugin self, string sid)
GeneAssociation
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
getGeneAssociation(long n)
Returns the GeneAssociation object that belongs to the given index. If the index is invalid, None
is returned.
n | the index number of the GeneAssociation to get. |
getGeneAssociation(string sid)
Returns the GeneAssociation object based on its identifier.
sid | a string representing the identifier of the GeneAssociation to get. |
sid
or None if no such GeneAssociation exists.
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inherited |
Python method signature(s):
getLevel(SBasePlugin self)long
Returns the SBML level of the package extension of this plugin object.
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inherited |
def libsbml.FbcModelPlugin.getListOfFluxBounds | ( | self, | |
args | |||
) |
Python method signature(s):
getListOfFluxBounds(FbcModelPlugin self)ListOfFluxBounds getListOfFluxBounds(FbcModelPlugin self)
ListOfFluxBounds
Returns the ListOfFluxBounds in this plugin object.
def libsbml.FbcModelPlugin.getListOfGeneAssociations | ( | self, | |
args | |||
) |
Python method signature(s):
getListOfGeneAssociations(FbcModelPlugin self)ListOfGeneAssociations getListOfGeneAssociations(FbcModelPlugin self)
ListOfGeneAssociations
Returns the ListOfObjectives in this plugin object.
def libsbml.FbcModelPlugin.getListOfObjectives | ( | self, | |
args | |||
) |
Python method signature(s):
getListOfObjectives(FbcModelPlugin self)ListOfObjectives getListOfObjectives(FbcModelPlugin self)
ListOfObjectives
Returns the ListOfObjectives in this plugin object.
def libsbml.FbcModelPlugin.getNumFluxBounds | ( | self | ) |
Python method signature(s):
getNumFluxBounds(FbcModelPlugin self)long
Returns the number of FluxBound object in this plugin object.
def libsbml.FbcModelPlugin.getNumGeneAssociations | ( | self | ) |
Python method signature(s):
getNumGeneAssociations(FbcModelPlugin self)int
Returns the number of GeneAssociation object in this plugin object.
def libsbml.FbcModelPlugin.getNumObjectives | ( | self | ) |
Python method signature(s):
getNumObjectives(FbcModelPlugin self)long
Returns the number of Objective object in this plugin object.
def libsbml.FbcModelPlugin.getObjective | ( | self, | |
args | |||
) |
Python method signature(s):
getObjective(FbcModelPlugin self, long n)Objective getObjective(FbcModelPlugin self, long n)
Objective getObjective(FbcModelPlugin self, string sid)
Objective getObjective(FbcModelPlugin self, string sid)
Objective
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
getObjective(long n)
Returns the Objective object that belongs to the given index. If the index is invalid, None
is returned.
n | the index number of the Objective to get. |
getObjective(string sid)
Returns the Objective object based on its identifier.
sid | a string representing the identifier of the Objective to get. |
sid
or None if no such Objective exists.
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inherited |
Python method signature(s):
getPackageName(SBasePlugin self)string
Returns the package name of this plugin object.
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inherited |
Python method signature(s):
getPackageVersion(SBasePlugin self)long
Returns the package version of the package extension of this plugin object.
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inherited |
Python method signature(s):
getParentSBMLObject(SBasePlugin self)SBase getParentSBMLObject(SBasePlugin self)
SBase
Returns the parent SBase object to which this plugin object connected.
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inherited |
Python method signature(s):
getPrefix(SBasePlugin self)string
Returns the prefix of the package extension of this plugin object.
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inherited |
Python method signature(s):
getSBMLDocument(SBasePlugin self)SBMLDocument getSBMLDocument(SBasePlugin self)
SBMLDocument
Returns the parent SBMLDocument of this plugin object.
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inherited |
Python method signature(s):
getURI(SBasePlugin self)string
Gets the URI to which this element belongs to. For example, all elements that belong to SBML Level 3 Version 1 Core must would have the URI 'http://www.sbml.org/sbml/level3/version1/core'; all elements that belong to Layout Extension Version 1 for SBML Level 3 Version 1 Core must would have the URI 'http://www.sbml.org/sbml/level3/version1/layout/version1/'
Unlike getElementNamespace, this function first returns the URI for this element by looking into the SBMLNamespaces object of the document with the its package name. if not found it will return the result of getElementNamespace
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inherited |
Python method signature(s):
getVersion(SBasePlugin self)long
Returns the SBML version of the package extension of this plugin object.
def libsbml.FbcModelPlugin.removeFluxBound | ( | self, | |
args | |||
) |
Python method signature(s):
removeFluxBound(FbcModelPlugin self, long n)FluxBound removeFluxBound(FbcModelPlugin self, string sid)
FluxBound
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
removeFluxBound(long n)
Removes the nth FluxBound object from this plugin object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
n | the index of the FluxBound object to remove |
None
is returned if the given index is out of range.removeFluxBound(string sid)
Removes the FluxBound object with the given sid
attribute from this plugin object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
sid | the id attribute of the FluxBound object to remove |
None
is returned if the given index is out of range. def libsbml.FbcModelPlugin.removeGeneAssociation | ( | self, | |
args | |||
) |
Python method signature(s):
removeGeneAssociation(FbcModelPlugin self, long n)GeneAssociation removeGeneAssociation(FbcModelPlugin self, string sid)
GeneAssociation
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
removeGeneAssociation(long n)
Removes the nth GeneAssociation object from this plugin object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
n | the index of the GeneAssociation object to remove |
None
is returned if the given index is out of range.removeGeneAssociation(string sid)
Removes the GeneAssociation object with the given sid
attribute from this plugin object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
sid | the id attribute of the GeneAssociation object to remove |
None
is returned if the given index is out of range. def libsbml.FbcModelPlugin.removeObjective | ( | self, | |
args | |||
) |
Python method signature(s):
removeObjective(FbcModelPlugin self, long n)Objective removeObjective(FbcModelPlugin self, string sid)
Objective
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
removeObjective(long n)
Removes the nth Objective object from this plugin object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
n | the index of the Objective object to remove |
None
is returned if the given index is out of range.removeObjective(string sid)
Removes the Objective object with the given sid
attribute from this plugin object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
sid | the id attribute of the Objective object to remove |
None
is returned if the given index is out of range. def libsbml.FbcModelPlugin.setActiveObjectiveId | ( | self, | |
args | |||
) |
Python method signature(s):
setActiveObjectiveId(FbcModelPlugin self, string objectiveId)int
Sets the id of the active objective.
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inherited |
Python method signature(s):
setElementNamespace(SBasePlugin self, string uri)int
Sets the XML namespace to which this element belongs to. For example, all elements that belong to SBML Level 3 Version 1 Core must set the namespace to 'http://www.sbml.org/sbml/level3/version1/core'; all elements that belong to Layout Extension Version 1 for SBML Level 3 Version 1 Core must set the namespace to 'http://www.sbml.org/sbml/level3/version1/layout/version1/'
def libsbml.FbcModelPlugin.unsetActiveObjectiveId | ( | self | ) |
Python method signature(s):
unsetActiveObjectiveId(FbcModelPlugin self)
Unsets the active objective.